Flow through arrays of cylinders is a common phenomenon in coastal engineering, particularly in nature-inspired systems such as coastal forests and mangroves, which mitigate tsunami and storm surge damage by dissipating flow energy. Pore flow behavior, including its energy dissipation, is strongly influenced by cylinder spacing: larger spacing permits vortex shedding and time-dependent fluctuations, whereas smaller spacing suppresses shedding, resulting in stable pore flow. This study investigated energy dissipation in cylinder array pores, focusing on the transition from steady to fluctuating flow induced by changes in the spacing between cylinders. Three-dimensional simulations were performed using the incompressible Navier–Stokes equations and the immersed boundary method. Twelve cases were computed, varying the Reynolds numbers (Re = 100, 200, 300) and spacings (Δl/D = 2.0, 2.5, 3.0, 4.0; D is the cylinder diameter). For Re = 100 and 200, vortex-shedding-induced pore low fluctuations emerged at Δl/D≥ 3.0, while for Re = 300, fluctuations appeared at Δl/D≥ 2.5. Results showed that overall viscous dissipation decreased with increasing spacing. In contrast, the fraction of dissipation attributable to flow fluctuations rose sharply from 0 to about 50% after the transition from steady to fluctuating flow, particularly for Re = 200 and 300. These findings underscore the significant contribution of unsteady pore flow to dissipation at larger spacings.